Last update on 21 March 2017
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The S3-Tools

UPDATE [06-07/03/2012] : A major bug was corrected that affected the line widths of all SAX sources mapped, in both HI and CO lines. Details on this bug can be found here. It is now corrected, so users who think they may have been affected should download the latest version of the S3Tools and rebuild their cubes. Sorry about any inconvenience.


INTRODUCTION
The SKA Simulated Skies (S3) Tools are a set of Python-based routines and interfaces whose purpose is to provide user-friendly access to the SKA Simulated Skies set of simulations, performed at the University of Oxford in the framework of the European Union's SKADS program. The S3 simulations are described on the S3 website and the databases built from these may be queried there. The S3 Tools may then be used on query results to build maps and spectral data cubes.

In order to use the S3 Tools, you will need a number of python modules : os, sys, getopt, math, numpy, scipy, pyfits, time, random, types, ctypes, stat, Image, Tkinter, tkFileDialog, tkFont, matplotlib. The install script described below first looks for the necessary packages and warns the user if some were not found. Depending on which package is missing, the limitations could go from not being able to build the plots when running tests to downright not being able to make maps at all. For Mac OS X users, the necessary packages should be included in the SciSoft package (version 2008.3.1 onwards) for Mac OS X.

INSTALLATION
To use the S3 Tools, you should follow these simple steps:
1. Download the S3Tools.tgz archive
2. Uncompress it in a directory of your choice.
3. Install the templates needed for your purposes (HI, CO, GSM, EoR,...). For detailed instructions, please see below.
4. Run the installation script install.py included in the distribution. Refer to the README file for details.

CONFIGURATION
For clarity, we shall assume that the S3-Tools were installed in ~/S3Tools/, that is, you have a S3Tools/ directory under your home folder, with subdirectories Config/, Doc/, Output/, Routines/ and Tmp/.

Setting the S3-Tools path
Edit the Config_Path.py file under ~/S3Tools/Config/, so that S3TOOLS_PATH be set to ~/S3Tools/.

HI and CO templates [University of Oxford]

These are templates for the HI and CO emission of galaxies, to use with S3-SAX, made by Danail Obreschkow. To use these :

1. Download the SAX_templates.tgz archive here.
2. Untar it in a directory of your choice, and edit the Config_Path.py file under ~/S3Tools/Config/, so that SAX_TEMPLATES_DIR be set to that directory.
3. If you have an older (predating March 2011) installation of these templates, you need to create a subdirectory named FITS/ into which FITS files for the templates will be placed. The original template files are ascii (under the ascii/ subdirectory) but they take a while to load into arrays, much longer than when read from FITS files. Consequently, when making SAX cubes, the script first looks for a FITS file, and uses that if it can find it. Otherwse, it uses the ascii file and takes the opportunity to convert it to FITS and save it under FITS/ for future use. The downside of that is that FITS files take up a much bigger disk space than ascii files.

HI templates [Kapteyn Institute]

These are templates for the HI emission of galaxies, to use with S3-SAX, made by Rense Boomsma. To use these :

1. Download the KI_templates.tgz archive here.
2. Untar it in a directory of your choice, and edit the Config_Path.py file under ~/S3Tools/Config/, so that KAPTEYN_TEMPLATES_DIR be set to that directory.

Global Sky Model [MIT]

This is a model of Galactic emission, made by de Oliveira-Costa et al. (2008). To use it :

1. Download the GSM routines and data from the GSM website.
2. Untar it in a directory of your choice, and edit the Config_Path.py file under ~/S3Tools/Config/, so that GSM_DIR be set to that directory.
3. Replace the gsm.f file in the distribution with a non-interactive one available here. Compile that file into a gsm executable, e.g. "g77 gsm.f -o gsm".

Epoch of Reionization [IST]

This is a model of the EoR signal, made by Mario Santos. To use it :

1. Download the EoR-Lisbon.tgz archive here.
2. Untar it in a directory of your choice, and edit the Config_Path.py file under ~/S3Tools/Config/, so that IST_EOR_TEMPLATES_DIR be set to that directory.

TESTING
A number of shell scripts are available to test the correct workings of the S3Tools. These require that you download the Tests.tgz archive, which holds reference input and output files used for testing. Tests performed include S3-SEX cubes, S3-SAX cubes using either Oxford and Kapteyn templates, Cosmic Microwave Background, Global Sky Model and noise. For more information, please refer to the README file or to the User's guide.

DOWNLOADS
S3Tools.tgz : Current S3-Tools distribution (last updated on 21 March 2017)
S3Tools.pdf : User's guide
README : Installation, configuration and testing README file
Tests.tgz : Reference input and output files for testing